The problem is pretty vague so it's difficult to help. There could be a variety of issues, including the problem existing outside of IE or explorer and just coincidentally starting when you upgraded the browser. Have you installed anything else recently?

Run 'msconfig' from the command line and under the startup tab carefully disable startup items that you are know the function for.
Pull items like real player, MS office startup, etc, etc out of there. Also, clean out your Startup folder found in the Start menu.

It's also possible that there's a plugin for IE installed that doesn't like the combination of its version with Win98 and the new IE6. If you have various plugins that are old, you might want to update them to the latest version.

If it's a problem specifically with IE, most of the time fixes like these do not work. If you have an easy means of backing up your data or not a lot of data to backup to begin with, I'd suggest a fresh install. Once those problems creep into IE itself, they seem to persist until you give in and reinstall.

Use system monitor from system tools to see how much of the CPU speed (kernel) is being used. Its possible that IE 6 is using up all of pc's speed and forces it to lock up or freeze, if that is what is happening. If it is high like near 100%, then your CPU may not be able to handle it. If that's the case, can you go back to IE 5.5 or use Netscape?